Molecular Morphology: Deep Phylogeny Using RNA Structures and Related Markers

我们建议继续重新评估现有的核糖体RNA数据和其他非编码RNA类，使用二级结构感知方法，重点放在将由DMP中其他参与研究小组执行的EST调查检索的数据。在这方面，我们将继续开发和改进算法，以推导出新的rRNA序列和其他合适的ncRNA类的可靠的二级结构模型，并开发利用二级结构本身的进化来重建系统发育的方法。将探索从多个序列比对中自主获得特定于支系的“分子形态特征”，例如序列特征，例如特别保守的模式或插入，以及具有系统发育信息的结构特征。开发和应用一个模型来解释ncRNA二级结构的特征进化，作为一个实用的结构比对工具，并考虑“现实的”突变事件，将是有意义的。此外，将开发区分保守区域和“其他”区域的核苷酸替代模型，并纳入结构元件本身较慢的进化。将探索基于结构的和结构增强的系统发育方法是否可以扩展到氨基酸序列。将向研究界提供基于rRNA的系统发育的新的和改进的软件。

We propose a continued re-evaluation of the existing ribosomal RNA data, and other non-coding RNA classes, with secondary-structure-aware methods, focusing on data that will be retrieved by the EST surveys performed by other participating research groups in the DMP. In this context, we will continue to develop and refine algorithms for the derivation of reliable secondary structure models of novel rRNA sequences and other suitable ncRNA classes, as well as develop methods for utilizing the evolution of the secondary structures themselves for reconstructing phylogenies. The autonomous derivation of clade-specific “molecular morphological characters”, such as sequence features, e.g. particularly wellconserved patterns or insertions, from multiple sequence alignments, and phylogenetically informative structural features will be explored. The development and application of a model that accounts for the character evolution of ncRNA secondary structure as a practical structural alignment tool and the consideration of “realistic” mutational events will be of interest. Additionally, nucleotide substitution models that distinguish between conserved and “other” regions, as well as incorporate the slower evolution of the structural elements themselves will be developed. It will be explored whether the structure-based and structure-enhanced phylogenetic methods can be extended to amino acid sequences. Novel and improved software for rRNA based phylogeny will be provided to the research community.